DNA Ligase

(All numbering and residues are taken from first PDB file)

Run Details Domains Sequence Morph Domain Pairs Contact Graph

DynDom run details

  Property   Value
  Name DNA Ligase
  Conformer 1
(PDB) 		6wbo (A)
  Conformer 2
(PDB) 		3gde (A)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)		 Residues
1 206 1.13   224 - 435
2 208 2.15   15 - 223
3 127 0.84   436 - 562

Sequence


           ________________________________________________________________________________________________________________________ 
 6wbo(A) : **HMRYSELAELYRRLEKTTLKTLKTKFVADFLKKTPD--DLLEIVPYLILGKVFPDWDERELGVGEKLLIKAVSMATGVPEKEIENSIKDTGDLGESVALALKKRRQKSFFSQPLTIKR 
         :                                                                                                                          
 3gde(A) : GSHMLFAEFAEFCERLEKISSTLELTARIAAFLQKIEDERDLYDVVLF-ITGKVYPPWDERELGVGIGLLYEALENVSGVKRSEIESMIREYGDLGLVAEQLIKKKKMTTLAFEELTVRK 
           ________________________________________________________________________________________________________________________ 

           ______________________________________________________________________________________________223_______________________ 
 6wbo(A) : VYNTFVKVAEASGEGSQDRKMKYLANLFMDAGPEEGKYIARTVLGTMRTGVAEGILRDAIAEAFKVKVELVERAYMLTSDFGYVAKIAKLEGNEGLSKVSIQIGKPIRPMLAQNAASVKD 
         :                                                                                                                          
 3gde(A) : VRETFDEIASLTGEGSMKRKIMLLTGLYGLATPLEARYLTRLILNEMRLGVGEGIMRDAIARAFRADPETVERAYMITNDLGRVAVVAKKEGEEGLRKMKIEIHIPVRMMLAQVAESLES 
           ______________________________________________________________________________________________213_______________________ 

           ________________________________________________________________________________________________________________________ 
 6wbo(A) : ALIEMGGEAAFEIKYDGARVQVHRDGDKVIIYSRRLENVTRSIPEIVEAVKASLKPSKVIVEGELVAVGENGRPRPFQYVLRRFRRKYNIEEMIEKIPLELNLFDILYVNGESLIDTKFT 
         :                                                                                                                          
 3gde(A) : AVREMR-TAAVEWKFDGSRVQVHWDGSRVTIYSRRLENVTNALPDIVEEIKKSVKPG-VILDGEVIAVKE-GKPMPFQHVLRRFRR--dVAKMVEKIPLEAHFFDILYHDGEC-IDLPLR 
           ________________________________________________________________________________________________________________________ 

           ______________________________________________________________431_______________________________________________________ 
 6wbo(A) : ERRKRLEESVEESDKIKLAEQLVTKKVDEAEEFYKRALELGHEGLMAKRLDAIYEPGNRGKKWLKIKPTMENLDLVIIGAEWGEGRRAHLLGSFLVGAYDPESGEFVPVGKVGSGFTDED 
         :                                                                                                                          
 3gde(A) : ERRKLLESAVNESEKIKLAKQIVTDSVDEVRKMYDEAISAGHEGVMIKLPSSPYIPGKRGKNWLKVKAIMETLDLVVVGGEWGEGKRSHWLSSFELACLDPVTGKLLKVGRVATGFTEED 
           ______________________________________________________________417_______________________________________________________ 

           _______________________________________________________________________________                                          
 6wbo(A) : LVEFTKMLKPLIIREEGKFVEIEPKVVIEVTYQEIQKSPKYKSGFALRFPRYVALRENKSPEEADTIERVAQLYELQER                                          
         :                                                                                                                          
 3gde(A) : LEELTEMFRPLIVSQQGKKVEFIPKYVFEVAYQEIQKSPKYESGYALRFPRFVRLRDDKDVDEADTIERVENLYKLQF*                                          
           _______________________________________________________________________________                                          

Morph

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Domain Pairs

Property Value
Fixed Domain
( blue ) 		1
Moving Domain
( red ) 		2
Rotation Angle
(deg) 		22.5
Translation
(A) 		-0.7
Closure
(%) 		93.8
Bending Residues
( green ) 		  223 - 224
Bending Region Analysis
Property Value
Fixed Domain
( blue ) 		1
Moving Domain
( yellow ) 		3
Rotation Angle
(deg) 		172.5
Translation
(A) 		0.8
Closure
(%) 		53.8
Bending Residues
( green ) 		  431 - 437
Bending Region Analysis

Dynamic Contact Graph

Conformer 1 Contact:
Residue 1 ———› Residue 2

Conformer 2 Contact:
Residue 2 ———› Residue 1

Movement classification: Mixed

Conformer 1 Contact:
Residue 1 ———› Residue 3

Conformer 2 Contact:
Residue 3 ———› Residue 1

Movement classification: Hinge

PyMOL Script

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